ProtocolBase (Kuali Coeus 5.1.1 API)

java.lang.Object
- org.kuali.rice.krad.bo.BusinessObjectBase
- - org.kuali.rice.krad.bo.PersistableBusinessObjectBase
  - - org.kuali.kra.bo.KraPersistableBusinessObjectBase
    - - org.kuali.kra.protocol.ProtocolBase

All Implemented Interfaces:

Serializable, org.apache.ojb.broker.PersistenceBrokerAware, Disclosurable, Permissionable, KcKrmsContextBo, Sequenceable, SequenceAssociate<ProtocolBase>, SequenceOwner<ProtocolBase>, UnitAclLoadable, org.kuali.rice.core.api.mo.common.GloballyUnique, org.kuali.rice.core.api.mo.common.Versioned, org.kuali.rice.core.api.mo.ModelObjectBasic, org.kuali.rice.krad.bo.BusinessObject, org.kuali.rice.krad.bo.PersistableBusinessObject

Direct Known Subclasses:

IacucProtocol, Protocol
```
public abstract class ProtocolBase
extends KraPersistableBusinessObjectBase
implements SequenceOwner<ProtocolBase>, Permissionable, UnitAclLoadable, Disclosurable, KcKrmsContextBo
```
See Also:
Serialized Form

Field Summary

Fields
Modifier and Type Field and Description

protected static CharSequence AMENDMENT_LETTER

protected static String NEXT_ACTION_ID_KEY

protected static CharSequence RENEWAL_LETTER
- Fields inherited from class org.kuali.kra.bo.KraPersistableBusinessObjectBase
  UPDATE_USER_LENGTH
- Fields inherited from class org.kuali.rice.krad.bo.PersistableBusinessObjectBase
  extension, versionNumber
- Fields inherited from interface org.kuali.kra.common.permissions.Permissionable
  AWARD_BUDGET_KEY, AWARD_KEY, COI_DISCLOSURE_KEY, COMMITTEE_KEY, COMMITTEE_SCHEDULE_KEY, IACUC_PROTOCOL_KEY, IACUC_PROTOCOL_ONLINE_REVIEW_KEY, NEGOTIATION_KEY, PROPOSAL_BUDGET_KEY, PROPOSAL_KEY, PROTOCOL_KEY, PROTOCOL_ONLINE_REVIEW_KEY, SPONSOR_HIREARCHY_KEY, SUBAWARD_KEY, TIME_AND_MONEY_KEY

Fields
Modifier and Type	Field and Description
`protected static CharSequence`	`AMENDMENT_LETTER`
`protected static String`	`NEXT_ACTION_ID_KEY`
`protected static CharSequence`	`RENEWAL_LETTER`

Constructor Summary

Constructors
Constructor and Description

ProtocolBase()
Constructs an ProtocolBase BO.

Constructors
Constructor and Description
`ProtocolBase()` Constructs an ProtocolBase BO.

Method Summary

Methods
Modifier and Type	Method and Description
`protected void`	`addAdditionalInfoSummary(ProtocolSummary protocolSummary)`
`<T extends ProtocolAttachmentBase> void`	`addAttachmentsByType(T attachment)` Adds a attachment to a ProtocolBase where the type of attachment is used to determine where to add the attachment.
`protected void`	`addAttachmentSummaries(ProtocolSummary protocolSummary)`
`protected void`	`addFundingSourceSummaries(ProtocolSummary protocolSummary)`
`protected void`	`addOrganizationSummaries(ProtocolSummary protocolSummary)`
`protected void`	`addPersonnelSummaries(ProtocolSummary protocolSummary)`
`void`	`addProtocolResearchAreas(ProtocolResearchAreaBase protocolResearchArea)`
`protected void`	`addResearchAreaSummaries(ProtocolSummary protocolSummary)`
`void`	`addSpecialReview(ProtocolSpecialReviewBase specialReview)`
`protected void`	`addSpecialReviewSummaries(ProtocolSummary protocolSummary)`
`protected void`	`amendQuestionnaire(ProtocolBase amendment)`
`List`	`buildListOfDeletionAwareLists()`
`void`	`cleanupSpecialReviews(ProtocolBase srcProtocol)`
`protected abstract ProtocolSummary`	`createProtocolSummary()`
`protected Object`	`deepCopy(Object obj)`
`List<CommitteeMembershipBase>`	`filterOutProtocolPersonnel(List<CommitteeMembershipBase> members)` This method will filter out this protocol's personnel from the given list of committee memberships
`List<ProtocolAttachmentProtocolBase>`	`getActiveAttachmentProtocols()` This method will return the list of all active attachments for this protocol; an attachment A is active for a protocol if either A has a doc status code of 'draft' or if for all other attachments for that protocol having the same doc id as A's doc id, none have a version number greater than A's version number.
`List<ProtocolAttachmentProtocolBase>`	`getActiveAttachmentProtocolsNoDelete()` This method will return the list of undeleted attachments that are still active for this protocol.
`String`	`getAmendedProtocolNumber()` If the protocol document is an amendment or renewal the parent protocol number is being returned.
`protected abstract List<AnswerHeader>`	`getAnswerHeaderForProtocol(ProtocolBase protocol)`
`Date`	`getApplicationDate()` This method is to return the first submission date as application date.
`Date`	`getApprovalDate()`
`List<ProtocolAttachmentPersonnelBase>`	`getAttachmentPersonnels()` Deprecated. Gets the attachment personnels. Cannot return `null`.
`ProtocolAttachmentProtocolBase`	`getAttachmentProtocol(int index)` Gets an attachment protocol.
`List<ProtocolAttachmentProtocolBase>`	`getAttachmentProtocols()` Gets the attachment protocols.
`protected org.kuali.rice.krad.service.BusinessObjectService`	`getBusinessObjectService()`
`String`	`getCorrespondentIndicator()`
`protected org.kuali.rice.core.api.datetime.DateTimeService`	`getDateTimeService()`
`String`	`getDefaultNewDescription()`
`protected abstract String`	`getDefaultProtocolStatusCodeHook()`
`protected abstract String`	`getDefaultProtocolTypeCodeHook()`
`String`	`getDescription()`
`abstract String`	`getDocumentKey()` This method returns unique key for implementing document.
`String`	`getDocumentNumberForPermission()` This method returns the appropriate document number for implementing documents For award it would be awardNumber and for PDD it would be proposal Number.
`abstract String`	`getDocumentRoleTypeCode()` Returns the type code of the document (i.e.
`String`	`getDocumentUnitNumber()` Returns the unit number of the unit to which the document belongs to.
`Date`	`getExpirationDate()`
`String`	`getFdaApplicationNumber()`
`List<ProtocolAttachmentProtocolBase>`	`getFilteredAttachmentProtocols()` This method returns a list of attachments which respect the sort filter
`String`	`getFundingSource()`
`String`	`getFundingSourceIndicator()`
`Date`	`getInitialSubmissionDate()`
`String`	`getInitiatorLastUpdated()`
`String`	`getInvestigator()`
`String`	`getKeyPerson()`
`String`	`getKeyStudyPersonIndicator()`
`Date`	`getLastApprovalDate()`
`ProtocolActionBase`	`getLastProtocolAction()`
`ProtocolUnitBase`	`getLeadUnit()`
`String`	`getLeadUnitName()`
`String`	`getLeadUnitNumber()`
`abstract String`	`getNamespace()`
`String`	`getNewDescription()`
`protected abstract ProtocolResearchAreaBase`	`getNewProtocolResearchAreaInstance()`
`Integer`	`getNextValue(String key)` Get the next value in a sequence.
`ProtocolNotepadBase`	`getNotepad(int index)` Gets an attachment protocol.
`List<ProtocolNotepadBase>`	`getNotepads()` Gets the notepads.
`Long`	`getNotifyIrbSubmissionId()`
`Integer`	`getOwnerSequenceNumber()` This method returns its owner's sequence number.
`org.kuali.rice.coreservice.framework.parameter.ParameterService`	`getParameterService()`
`String`	`getPerformingOrganizationId()`
`ProtocolPersonBase`	`getPrincipalInvestigator()` This method is to find Principal Investigator from ProtocolPersonBase list
`String`	`getPrincipalInvestigatorId()`
`String`	`getPrincipalInvestigatorName()`
`String`	`getProjectId()` This method to get project number
`String`	`getProjectName()` This method is mainly to get the title
`List<ProtocolActionBase>`	`getProtocolActions()`
`ProtocolAmendRenewalBase`	`getProtocolAmendRenewal()`
`List<ProtocolAmendRenewalBase>`	`getProtocolAmendRenewals()`
`ProtocolAttachmentFilterBase`	`getProtocolAttachmentFilter()`
`protected abstract Class<? extends ProtocolAttachmentProtocolBase>`	`getProtocolAttachmentProtocolClassHook()`
`ProtocolDocumentBase`	`getProtocolDocument()`
`List<ProtocolFundingSourceBase>`	`getProtocolFundingSources()`
`Long`	`getProtocolId()`
`List<ProtocolLocationBase>`	`getProtocolLocations()`
`protected ProtocolLocationService`	`getProtocolLocationService()` This method is to get protocol location service
`protected abstract String`	`getProtocolModuleAddModifyAttachmentCodeHook()`
`String`	`getProtocolNumber()`
`List<ProtocolOnlineReviewBase>`	`getProtocolOnlineReviews()` Collects and returns all online reviews for all submissions for this protocol.
`ProtocolPersonBase`	`getProtocolPerson(int index)` Gets index i from the protocol person list.
`protected abstract ProtocolPersonnelService`	`getProtocolPersonnelService()` This method is a hook to get actual protocol personnel service impl corresponding to the protocol type
`List<ProtocolPersonBase>`	`getProtocolPersons()`
`List<ProtocolReferenceBase>`	`getProtocolReferences()`
`List<ProtocolResearchAreaBase>`	`getProtocolResearchAreas()`
`ProtocolResearchAreaBase`	`getProtocolResearchAreas(int index)`
`ProtocolStatusBase`	`getProtocolStatus()`
`String`	`getProtocolStatusCode()`
`protected abstract ProtocolStatusBase`	`getProtocolStatusNewInstanceHook()`
`ProtocolSubmissionBase`	`getProtocolSubmission()`
`protected abstract ProtocolSubmissionBase`	`getProtocolSubmissionNewInstanceHook()`
`List<ProtocolSubmissionBase>`	`getProtocolSubmissions()`
`String`	`getProtocolSubmissionStatus()`
`protected abstract ProtocolSubmissionStatusBase`	`getProtocolSubmissionStatusNewInstanceHook()`
`protected abstract ProtocolSubmissionTypeBase`	`getProtocolSubmissionTypeNewInstanceHook()`
`abstract ProtocolSummary`	`getProtocolSummary()`
`ProtocolTypeBase`	`getProtocolType()`
`String`	`getProtocolTypeCode()`
`protected QuestionnaireAnswerService`	`getQuestionnaireAnswerService()`
`String`	`getReferenceIndicator()`
`String`	`getReferenceNumber1()`
`String`	`getReferenceNumber2()`
`String`	`getRelatedProjectsIndicator()`
`String`	`getResearchAreaCode()`
`abstract List<String>`	`getRoleNames()` This method gets all the role names for particular document.
`protected org.kuali.rice.krad.service.SequenceAccessorService`	`getSequenceAccessorService()`
`Integer`	`getSequenceNumber()` This gets the current version number.
`ProtocolBase`	`getSequenceOwner()` The SequenceOwner is returned; "this" should be returned if this associate is the sequence owner.
`List<ProtocolActionBase>`	`getSortedActions()`
`ProtocolSpecialReviewBase`	`getSpecialReview(int index)`
`String`	`getSpecialReviewIndicator()`
`List<ProtocolSpecialReviewBase>`	`getSpecialReviews()`
`Date`	`getSubmissionDate()` Gets the submission date.
`String`	`getTitle()`
`String`	`getVersionNameField()` For Award, this would be "awardNumber", for Committee "committeeName", for Protocol "protocolNumber", etc.
`void`	`incrementSequenceNumber()` This increments sequence number on an owner of a sequence.
`abstract void`	`initializeProtocolAttachmentFilter()`
`boolean`	`isActive()`
`boolean`	`isAmendment()`
`boolean`	`isCorrectionMode()`
`boolean`	`isEmptyProtocolResearchAreas()`
`boolean`	`isFollowupAction(String actionTypeCode)` This method is to check if the actiontypecode is a followup action.
`boolean`	`isLookupActionAmendRenewProtocol()`
`boolean`	`isLookupActionRequestProtocol()`
`boolean`	`isLookupPendingPIActionProtocol()`
`boolean`	`isLookupPendingProtocol()`
`boolean`	`isLookupProtocolPersonId()`
`boolean`	`isMemberInProtocolPersonnel(CommitteeMembershipBase member)` This method encapsulates the logic to decide if a committee member appears in the list of protocol personnel.
`boolean`	`isMergeAmendment()`
`boolean`	`isNew()`
`boolean`	`isNonEmployeeFlag()`
`boolean`	`isRenewal()`
`boolean`	`isRenewalWithoutAmendment()`
`boolean`	`isUserNamedInProtocol(String principalName)`
`boolean`	`isVersioningRequired()` Decides whether or not the ProtocolBase is in a state where changes will require versioning.
`void`	`merge(ProtocolBase amendment)` This method merges the data of the amended protocol into this protocol.
`void`	`merge(ProtocolBase amendment, boolean mergeActions)`
`abstract void`	`merge(ProtocolBase amendment, String protocolModuleTypeCode)`
`protected void`	`mergeAttachments(ProtocolBase amendment)`
`protected void`	`mergeFundingSources(ProtocolBase amendment)`
`protected void`	`mergeGeneralInfo(ProtocolBase amendment)`
`protected void`	`mergeNotepads(ProtocolBase amendment)`
`protected void`	`mergeOrganizations(ProtocolBase amendment)`
`protected void`	`mergeOthers(ProtocolBase amendment)`
`protected void`	`mergePersonnel(ProtocolBase amendment)`
`protected abstract void`	`mergeProtocolAction(ProtocolBase amendment)`
`protected void`	`mergeProtocolPermissions(ProtocolBase amendment)`
`protected void`	`mergeProtocolQuestionnaire(ProtocolBase amendment)`
`protected void`	`mergeProtocolSubmission(ProtocolBase amendment)`
`protected void`	`mergeReferences(ProtocolBase amendment)`
`protected void`	`mergeResearchAreas(ProtocolBase amendment)`
`protected void`	`mergeSpecialReview(ProtocolBase amendment)`
`void`	`populateAdditionalQualifiedRoleAttributes(Map<String,String> qualifiedRoleAttributes)` Allows a permissionable to set additional qualified role attributes that may be needed by kim services to resolve the role members.
`<T extends ProtocolAttachmentBase> void`	`removeAttachmentsByType(T attachment)` removes an attachment to a ProtocolBase where the type of attachment is used to determine where to add the attachment.
`protected void`	`removeOldQuestionnaire()`
`void`	`resetForeignKeys()`
`void`	`resetPersistenceState()` This method resets the persistence state used to establish whether this is a new entity or an already-persisted entity.
`void`	`resetPersistenceStateForNotifications()`
`protected void`	`restoreAttachments(ProtocolBase protocol)`
`void`	`setActive(boolean active)`
`void`	`setApprovalDate(Date approvalDate)`
`void`	`setAttachmentProtocols(List<ProtocolAttachmentProtocolBase> attachmentProtocols)`
`void`	`setCorrectionMode(boolean correctionMode)`
`void`	`setCorrespondentIndicator(String correspondentIndicator)`
`void`	`setDescription(String description)`
`void`	`setExpirationDate(Date expirationDate)`
`void`	`setFdaApplicationNumber(String fdaApplicationNumber)`
`void`	`setFundingSource(String fundingSource)`
`void`	`setFundingSourceIndicator(String fundingSourceIndicator)`
`void`	`setInitialSubmissionDate(Date initialSubmissionDate)`
`void`	`setInvestigator(String investigator)`
`void`	`setKeyPerson(String keyPerson)`
`void`	`setKeyStudyPersonIndicator(String keyStudyPersonIndicator)`
`void`	`setLastApprovalDate(Date lastApprovalDate)`
`void`	`setLeadUnitName(String leadUnitName)`
`void`	`setLeadUnitNumber(String leadUnitNumber)`
`void`	`setLookupActionAmendRenewProtocol(boolean lookupActionAmendRenewProtocol)`
`void`	`setLookupActionRequestProtocol(boolean lookupActionRequestProtocol)`
`void`	`setLookupPendingPIActionProtocol(boolean lookupPendingPIActionProtocol)`
`void`	`setLookupPendingProtocol(boolean lookupPendingProtocol)`
`void`	`setLookupProtocolPersonId(boolean lookupProtocolPersonId)`
`void`	`setMergeAmendment(boolean mergeAmendment)`
`void`	`setNewDescription(String newDescription)`
`void`	`setNonEmployeeFlag(boolean nonEmployeeFlag)`
`void`	`setNotepads(List<ProtocolNotepadBase> notepads)`
`void`	`setNotifyIrbSubmissionId(Long notifyIrbSubmissionId)`
`void`	`setPerformingOrganizationId(String performingOrganizationId)`
`void`	`setPrincipalInvestigatorId(String principalInvestigatorId)`
`void`	`setProtocolActions(List<ProtocolActionBase> protocolActions)`
`void`	`setProtocolAmendRenewal(ProtocolAmendRenewalBase amendRenewal)`
`void`	`setProtocolAmendRenewals(List<ProtocolAmendRenewalBase> protocolAmendRenewals)`
`void`	`setProtocolAttachmentFilter(ProtocolAttachmentFilterBase protocolAttachmentFilter)`
`void`	`setProtocolDocument(ProtocolDocumentBase protocolDocument)`
`void`	`setProtocolFundingSources(List<ProtocolFundingSourceBase> protocolFundingSources)`
`void`	`setProtocolId(Long protocolId)`
`void`	`setProtocolLocations(List<ProtocolLocationBase> protocolLocations)`
`void`	`setProtocolNumber(String protocolNumber)`
`void`	`setProtocolPersons(List<ProtocolPersonBase> protocolPersons)`
`void`	`setProtocolReferences(List<ProtocolReferenceBase> protocolReferences)`
`void`	`setProtocolResearchAreas(List<ProtocolResearchAreaBase> protocolResearchAreas)`
`void`	`setProtocolStatus(ProtocolStatusBase protocolStatus)`
`void`	`setProtocolStatusCode(String protocolStatusCode)`
`void`	`setProtocolSubmission(ProtocolSubmissionBase protocolSubmission)`
`void`	`setProtocolSubmissions(List<ProtocolSubmissionBase> protocolSubmissions)`
`void`	`setProtocolType(ProtocolTypeBase protocolType)`
`void`	`setProtocolTypeCode(String protocolTypeCode)`
`void`	`setReferenceIndicator(String referenceIndicator)`
`void`	`setReferenceNumber1(String referenceNumber1)`
`void`	`setReferenceNumber2(String referenceNumber2)`
`void`	`setRelatedProjectsIndicator(String relatedProjectsIndicator)`
`void`	`setResearchAreaCode(String researchAreaCode)`
`void`	`setSequenceNumber(Integer sequenceNumber)`
`void`	`setSequenceOwner(ProtocolBase newOwner)` This sets the sequence owner on the associate.
`void`	`setSpecialReviewIndicator(String specialReviewIndicator)`
`void`	`setSpecialReviews(List<ProtocolSpecialReviewBase> specialReviews)`
`void`	`setTitle(String title)`

Methods inherited from class org.kuali.kra.bo.KraPersistableBusinessObjectBase
getAuthorPersonName, getKcPersonService, getUpdateTimestamp, getUpdateUser, isUpdateUserSet, postPersist, prePersist, preUpdate, setUpdateTimestamp, setUpdateUser, setUpdateUserSet

Methods inherited from class org.kuali.rice.krad.bo.PersistableBusinessObjectBase
afterDelete, afterInsert, afterLookup, afterUpdate, beforeDelete, beforeInsert, beforeUpdate, getExtension, getObjectId, getPersistenceService, getPersistenceStructureService, getVersionNumber, isNewCollectionRecord, linkEditableUserFields, postLoad, postRemove, postUpdate, preRemove, refresh, refreshNonUpdateableReferences, refreshReferenceObject, setExtension, setNewCollectionRecord, setObjectId, setVersionNumber

Methods inherited from class org.kuali.rice.krad.bo.BusinessObjectBase
toString

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.kuali.kra.krms.KcKrmsContextBo
getKrmsRulesContext

Methods inherited from interface org.kuali.rice.core.api.mo.ModelObjectBasic
toString

Field Detail

AMENDMENT_LETTER

protected static final CharSequence AMENDMENT_LETTER

RENEWAL_LETTER

protected static final CharSequence RENEWAL_LETTER

NEXT_ACTION_ID_KEY

protected static final String NEXT_ACTION_ID_KEY

See Also:: Constant Field Values

Constructor Detail
- ProtocolBase
```
public ProtocolBase()
```
  Constructs an ProtocolBase BO.

Method Detail

getInitiatorLastUpdated

public String getInitiatorLastUpdated()

getProtocolSubmissionStatus

public String getProtocolSubmissionStatus()

getProtocolStatusNewInstanceHook

protected abstract ProtocolStatusBase getProtocolStatusNewInstanceHook()

getDefaultProtocolStatusCodeHook

protected abstract String getDefaultProtocolStatusCodeHook()

getDefaultProtocolTypeCodeHook

protected abstract String getDefaultProtocolTypeCodeHook()

getProtocolId
```
public Long getProtocolId()
```

setProtocolId

public void setProtocolId(Long protocolId)

getProtocolNumber
```
public String getProtocolNumber()
```

setProtocolNumber

public void setProtocolNumber(String protocolNumber)

getSequenceNumber
```
public Integer getSequenceNumber()
```
Description copied from interface: Sequenceable

This gets the current version number.

Specified by:

getSequenceNumber in interface Sequenceable

Returns:
the sequence number

setSequenceNumber

public void setSequenceNumber(Integer sequenceNumber)

setActive

public void setActive(boolean active)

isActive
```
public boolean isActive()
```

getProtocolTypeCode
```
public String getProtocolTypeCode()
```

setProtocolTypeCode

public void setProtocolTypeCode(String protocolTypeCode)

getProtocolStatusCode
```
public String getProtocolStatusCode()
```

setProtocolStatusCode

public void setProtocolStatusCode(String protocolStatusCode)

getTitle
```
public String getTitle()
```

setTitle
```
public void setTitle(String title)
```

getDescription
```
public String getDescription()
```

setDescription

public void setDescription(String description)

getSubmissionDate
```
public Date getSubmissionDate()
```
Gets the submission date. If the submission date is the last submission for the protocol. If the protocol has not been submitted, null is returned.

Returns:
the submission date or null if not yet submitted

getInitialSubmissionDate

public Date getInitialSubmissionDate()

setInitialSubmissionDate

public void setInitialSubmissionDate(Date initialSubmissionDate)

getApprovalDate
```
public Date getApprovalDate()
```

setApprovalDate

public void setApprovalDate(Date approvalDate)

getExpirationDate
```
public Date getExpirationDate()
```

setExpirationDate

public void setExpirationDate(Date expirationDate)

getLastApprovalDate
```
public Date getLastApprovalDate()
```

setLastApprovalDate

public void setLastApprovalDate(Date lastApprovalDate)

getFdaApplicationNumber

public String getFdaApplicationNumber()

setFdaApplicationNumber

public void setFdaApplicationNumber(String fdaApplicationNumber)

getReferenceNumber1
```
public String getReferenceNumber1()
```

setReferenceNumber1

public void setReferenceNumber1(String referenceNumber1)

getReferenceNumber2
```
public String getReferenceNumber2()
```

setReferenceNumber2

public void setReferenceNumber2(String referenceNumber2)

getSpecialReviewIndicator

public String getSpecialReviewIndicator()

setSpecialReviewIndicator

public void setSpecialReviewIndicator(String specialReviewIndicator)

getKeyStudyPersonIndicator

public String getKeyStudyPersonIndicator()

setKeyStudyPersonIndicator

public void setKeyStudyPersonIndicator(String keyStudyPersonIndicator)

getFundingSourceIndicator

public String getFundingSourceIndicator()

setFundingSourceIndicator

public void setFundingSourceIndicator(String fundingSourceIndicator)

getCorrespondentIndicator

public String getCorrespondentIndicator()

setCorrespondentIndicator

public void setCorrespondentIndicator(String correspondentIndicator)

getReferenceIndicator
```
public String getReferenceIndicator()
```

setReferenceIndicator

public void setReferenceIndicator(String referenceIndicator)

getRelatedProjectsIndicator

public String getRelatedProjectsIndicator()

setRelatedProjectsIndicator

public void setRelatedProjectsIndicator(String relatedProjectsIndicator)

getProtocolOnlineReviews
```
public List<ProtocolOnlineReviewBase> getProtocolOnlineReviews()
```
Collects and returns all online reviews for all submissions for this protocol.

Returns:
all online reviews for this protocol

getProtocolStatus

public ProtocolStatusBase getProtocolStatus()

setProtocolStatus

public void setProtocolStatus(ProtocolStatusBase protocolStatus)

getProtocolType

public ProtocolTypeBase getProtocolType()

setProtocolType

public void setProtocolType(ProtocolTypeBase protocolType)

getNewDescription
```
public String getNewDescription()
```

setNewDescription

public void setNewDescription(String newDescription)

getDefaultNewDescription

public String getDefaultNewDescription()

setProtocolResearchAreas

public void setProtocolResearchAreas(List<ProtocolResearchAreaBase> protocolResearchAreas)

getProtocolResearchAreas

public List<ProtocolResearchAreaBase> getProtocolResearchAreas()

addProtocolResearchAreas

public void addProtocolResearchAreas(ProtocolResearchAreaBase protocolResearchArea)

getProtocolResearchAreas

public ProtocolResearchAreaBase getProtocolResearchAreas(int index)

getNewProtocolResearchAreaInstance

protected abstract ProtocolResearchAreaBase getNewProtocolResearchAreaInstance()

setProtocolReferences

public void setProtocolReferences(List<ProtocolReferenceBase> protocolReferences)

getProtocolReferences

public List<ProtocolReferenceBase> getProtocolReferences()

getProtocolDocument

public ProtocolDocumentBase getProtocolDocument()

setProtocolDocument

public void setProtocolDocument(ProtocolDocumentBase protocolDocument)

setProtocolLocations

public void setProtocolLocations(List<ProtocolLocationBase> protocolLocations)

getProtocolLocations

public List<ProtocolLocationBase> getProtocolLocations()

buildListOfDeletionAwareLists
```
public List buildListOfDeletionAwareLists()
```
Specified by:

buildListOfDeletionAwareLists in interface org.kuali.rice.krad.bo.PersistableBusinessObject

Overrides:

buildListOfDeletionAwareLists in class org.kuali.rice.krad.bo.PersistableBusinessObjectBase

getPrincipalInvestigator
```
public ProtocolPersonBase getPrincipalInvestigator()
```
This method is to find Principal Investigator from ProtocolPersonBase list

Returns:
ProtocolPersonBase

getPrincipalInvestigatorName

public String getPrincipalInvestigatorName()

getLeadUnit
```
public ProtocolUnitBase getLeadUnit()
```

getLeadUnitNumber
```
public String getLeadUnitNumber()
```
Specified by:

getLeadUnitNumber in interface Permissionable

setLeadUnitNumber

public void setLeadUnitNumber(String leadUnitNumber)

getPrincipalInvestigatorId

public String getPrincipalInvestigatorId()

setPrincipalInvestigatorId

public void setPrincipalInvestigatorId(String principalInvestigatorId)

isNonEmployeeFlag
```
public boolean isNonEmployeeFlag()
```

setNonEmployeeFlag

public void setNonEmployeeFlag(boolean nonEmployeeFlag)

getProtocolLocationService
```
protected ProtocolLocationService getProtocolLocationService()
```
This method is to get protocol location service

Returns:
ProtocolLocationService

getProtocolPersons

public List<ProtocolPersonBase> getProtocolPersons()

setProtocolPersons

public void setProtocolPersons(List<ProtocolPersonBase> protocolPersons)

getProtocolPerson
```
public ProtocolPersonBase getProtocolPerson(int index)
```
Gets index i from the protocol person list.

Parameters:
index -

Returns:
protocol person at index i

getProtocolPersonnelService
```
protected abstract ProtocolPersonnelService getProtocolPersonnelService()
```
This method is a hook to get actual protocol personnel service impl corresponding to the protocol type

Returns:
protocolPersonnelService

getProtocolFundingSources

public List<ProtocolFundingSourceBase> getProtocolFundingSources()

setProtocolFundingSources

public void setProtocolFundingSources(List<ProtocolFundingSourceBase> protocolFundingSources)

getResearchAreaCode
```
public String getResearchAreaCode()
```

setResearchAreaCode

public void setResearchAreaCode(String researchAreaCode)

getFundingSource
```
public String getFundingSource()
```

setFundingSource

public void setFundingSource(String fundingSource)

getPerformingOrganizationId

public String getPerformingOrganizationId()

setPerformingOrganizationId

public void setPerformingOrganizationId(String performingOrganizationId)

getLeadUnitName
```
public String getLeadUnitName()
```

setLeadUnitName

public void setLeadUnitName(String leadUnitName)

setSpecialReviews

public void setSpecialReviews(List<ProtocolSpecialReviewBase> specialReviews)

addSpecialReview
```
public void addSpecialReview(ProtocolSpecialReviewBase specialReview)
```
See Also:
org.kuali.kra.document.SpecialReviewHandler#addSpecialReview(org.kuali.kra.bo.AbstractSpecialReview)

getSpecialReview
```
public ProtocolSpecialReviewBase getSpecialReview(int index)
```
See Also:
org.kuali.kra.document.SpecialReviewHandler#getSpecialReview(int)

getSpecialReviews
```
public List<ProtocolSpecialReviewBase> getSpecialReviews()
```
See Also:
org.kuali.kra.document.SpecialReviewHandler#getSpecialReviews()

getAttachmentProtocols
```
public List<ProtocolAttachmentProtocolBase> getAttachmentProtocols()
```
Gets the attachment protocols. Cannot return null.

Returns:
the attachment protocols

getAttachmentProtocol
```
public ProtocolAttachmentProtocolBase getAttachmentProtocol(int index)
```
Gets an attachment protocol.

Parameters:
index - the index

Returns:
an attachment protocol

getNotepads
```
public List<ProtocolNotepadBase> getNotepads()
```
Gets the notepads. Cannot return null.

Returns:
the notepads

getNotepad
```
public ProtocolNotepadBase getNotepad(int index)
```
Gets an attachment protocol.

Parameters:
index - the index

Returns:
an attachment protocol

getAttachmentPersonnels
```
@Deprecated
public List<ProtocolAttachmentPersonnelBase> getAttachmentPersonnels()
```
Deprecated. Gets the attachment personnels. Cannot return null.

Returns:
the attachment personnels

addAttachmentsByType
```
public <T extends ProtocolAttachmentBase> void addAttachmentsByType(T attachment)
```
Adds a attachment to a ProtocolBase where the type of attachment is used to determine where to add the attachment.

Parameters:
attachment - the attachment

Throws:

IllegalArgumentException - if attachment is null or if an unsupported attachment is found

removeAttachmentsByType
```
public <T extends ProtocolAttachmentBase> void removeAttachmentsByType(T attachment)
```
removes an attachment to a ProtocolBase where the type of attachment is used to determine where to add the attachment.

Parameters:
attachment - the attachment

Throws:

IllegalArgumentException - if attachment is null or if an unsupported attachment is found

getKeyPerson
```
public String getKeyPerson()
```

setKeyPerson

public void setKeyPerson(String keyPerson)

getInvestigator
```
public String getInvestigator()
```

setInvestigator

public void setInvestigator(String investigator)

getProtocolSubmission

public ProtocolSubmissionBase getProtocolSubmission()

getProtocolSubmissionStatusNewInstanceHook

protected abstract ProtocolSubmissionStatusBase getProtocolSubmissionStatusNewInstanceHook()

getProtocolSubmissionTypeNewInstanceHook

protected abstract ProtocolSubmissionTypeBase getProtocolSubmissionTypeNewInstanceHook()

getProtocolSubmissionNewInstanceHook

protected abstract ProtocolSubmissionBase getProtocolSubmissionNewInstanceHook()

setProtocolSubmission

public void setProtocolSubmission(ProtocolSubmissionBase protocolSubmission)

setProtocolActions

public void setProtocolActions(List<ProtocolActionBase> protocolActions)

getProtocolActions

public List<ProtocolActionBase> getProtocolActions()

getLastProtocolAction

public ProtocolActionBase getLastProtocolAction()

setProtocolSubmissions

public void setProtocolSubmissions(List<ProtocolSubmissionBase> protocolSubmissions)

getProtocolSubmissions

public List<ProtocolSubmissionBase> getProtocolSubmissions()

getNextValue
```
public Integer getNextValue(String key)
```
Get the next value in a sequence.

Parameters:
key - the unique key of the sequence

Returns:
the next value

setAttachmentProtocols

public void setAttachmentProtocols(List<ProtocolAttachmentProtocolBase> attachmentProtocols)

setNotepads

public void setNotepads(List<ProtocolNotepadBase> notepads)

setProtocolAmendRenewal

public void setProtocolAmendRenewal(ProtocolAmendRenewalBase amendRenewal)

getProtocolAmendRenewal

public ProtocolAmendRenewalBase getProtocolAmendRenewal()

getProtocolAmendRenewals

public List<ProtocolAmendRenewalBase> getProtocolAmendRenewals()

setProtocolAmendRenewals

public void setProtocolAmendRenewals(List<ProtocolAmendRenewalBase> protocolAmendRenewals)

getOwnerSequenceNumber
```
public Integer getOwnerSequenceNumber()
```
This method returns its owner's sequence number. If this is the top level owner; i.e. Protocol or Award, it should return null

Specified by:

getOwnerSequenceNumber in interface SequenceOwner<ProtocolBase>

Returns:
the owner's sequence number

getVersionNameField
```
public String getVersionNameField()
```
Description copied from interface: SequenceOwner

For Award, this would be "awardNumber", for Committee "committeeName", for Protocol "protocolNumber", etc.

Specified by:

getVersionNameField in interface SequenceOwner<ProtocolBase>

Returns:
the field name that versions are "grouped" by
See Also:
SequenceOwner.getVersionNameField()

incrementSequenceNumber
```
public void incrementSequenceNumber()
```
This increments sequence number on an owner of a sequence.

Specified by:

incrementSequenceNumber in interface SequenceOwner<ProtocolBase>

getSequenceOwner
```
public ProtocolBase getSequenceOwner()
```
The SequenceOwner is returned; "this" should be returned if this associate is the sequence owner.

Specified by:

getSequenceOwner in interface SequenceAssociate<ProtocolBase>

Returns:
the SequenceOwner

setSequenceOwner
```
public void setSequenceOwner(ProtocolBase newOwner)
```
This sets the sequence owner on the associate. Should no-op if this associate has no sequence owner

Specified by:

setSequenceOwner in interface SequenceAssociate<ProtocolBase>

resetPersistenceState
```
public void resetPersistenceState()
```
This method resets the persistence state used to establish whether this is a new entity or an already-persisted entity. During sequencing, the VersioningService needs to be able to signal that a Sequenceable has changed state from an persisted entity to a new, unpersisted one. Otherwise, versioning operations would result earlier SequenceOwners losing the association with older versions of associates. This behavior comes into play whenever an associated object is versioned. Typically, implementers will set primary key fields to null to trigger an INSERT during save.

Specified by:

resetPersistenceState in interface Sequenceable

merge
```
public void merge(ProtocolBase amendment)
```
This method merges the data of the amended protocol into this protocol.

Parameters:
amendment -

merge

public void merge(ProtocolBase amendment,
         boolean mergeActions)

getProtocolModuleAddModifyAttachmentCodeHook

protected abstract String getProtocolModuleAddModifyAttachmentCodeHook()

merge

public abstract void merge(ProtocolBase amendment,
         String protocolModuleTypeCode)

mergeProtocolQuestionnaire

protected void mergeProtocolQuestionnaire(ProtocolBase amendment)

removeOldQuestionnaire

protected void removeOldQuestionnaire()

amendQuestionnaire

protected void amendQuestionnaire(ProtocolBase amendment)

getAnswerHeaderForProtocol

protected abstract List<AnswerHeader> getAnswerHeaderForProtocol(ProtocolBase protocol)

getQuestionnaireAnswerService

protected QuestionnaireAnswerService getQuestionnaireAnswerService()

getBusinessObjectService

protected org.kuali.rice.krad.service.BusinessObjectService getBusinessObjectService()

mergeProtocolSubmission

protected void mergeProtocolSubmission(ProtocolBase amendment)

mergeProtocolAction

protected abstract void mergeProtocolAction(ProtocolBase amendment)

mergeGeneralInfo

protected void mergeGeneralInfo(ProtocolBase amendment)

mergeResearchAreas

protected void mergeResearchAreas(ProtocolBase amendment)

mergeFundingSources

protected void mergeFundingSources(ProtocolBase amendment)

mergeReferences

protected void mergeReferences(ProtocolBase amendment)

mergeOrganizations

protected void mergeOrganizations(ProtocolBase amendment)

mergeAttachments

protected void mergeAttachments(ProtocolBase amendment)

restoreAttachments

protected void restoreAttachments(ProtocolBase protocol)

getProtocolAttachmentProtocolClassHook

protected abstract Class<? extends ProtocolAttachmentProtocolBase> getProtocolAttachmentProtocolClassHook()

mergeNotepads

protected void mergeNotepads(ProtocolBase amendment)

mergeSpecialReview

protected void mergeSpecialReview(ProtocolBase amendment)

mergePersonnel

protected void mergePersonnel(ProtocolBase amendment)

mergeOthers

protected void mergeOthers(ProtocolBase amendment)

mergeProtocolPermissions

protected void mergeProtocolPermissions(ProtocolBase amendment)

deepCopy

protected Object deepCopy(Object obj)

getProtocolSummary

public abstract ProtocolSummary getProtocolSummary()

addAdditionalInfoSummary

protected void addAdditionalInfoSummary(ProtocolSummary protocolSummary)

addSpecialReviewSummaries

protected void addSpecialReviewSummaries(ProtocolSummary protocolSummary)

addOrganizationSummaries

protected void addOrganizationSummaries(ProtocolSummary protocolSummary)

addFundingSourceSummaries

protected void addFundingSourceSummaries(ProtocolSummary protocolSummary)

addAttachmentSummaries

protected void addAttachmentSummaries(ProtocolSummary protocolSummary)

addResearchAreaSummaries

protected void addResearchAreaSummaries(ProtocolSummary protocolSummary)

addPersonnelSummaries

protected void addPersonnelSummaries(ProtocolSummary protocolSummary)

createProtocolSummary

protected abstract ProtocolSummary createProtocolSummary()

getDocumentKey
```
public abstract String getDocumentKey()
```
Description copied from interface: Permissionable

This method returns unique key for implementing document.

Specified by:

getDocumentKey in interface Permissionable

Returns:
See Also:
Permissionable.getDocumentKey()

getDocumentNumberForPermission
```
public String getDocumentNumberForPermission()
```
Description copied from interface: Permissionable

This method returns the appropriate document number for implementing documents For award it would be awardNumber and for PDD it would be proposal Number.

Specified by:

getDocumentNumberForPermission in interface Permissionable

Returns:
See Also:
Permissionable.getDocumentNumberForPermission()

getRoleNames
```
public abstract List<String> getRoleNames()
```
Description copied from interface: Permissionable

This method gets all the role names for particular document.

Specified by:

getRoleNames in interface Permissionable

Returns:
See Also:
Permissionable.getRoleNames()

resetForeignKeys
```
public void resetForeignKeys()
```

resetPersistenceStateForNotifications

public void resetPersistenceStateForNotifications()

getNamespace
```
public abstract String getNamespace()
```
Specified by:

getNamespace in interface Permissionable

getDocumentUnitNumber
```
public String getDocumentUnitNumber()
```
Description copied from interface: UnitAclLoadable

Returns the unit number of the unit to which the document belongs to.

Specified by:

getDocumentUnitNumber in interface UnitAclLoadable

Returns:
unitNumber of document
See Also:
org.kuali.kra.UnitAclLoadable#getUnitNumberOfDocument()

getDocumentRoleTypeCode
```
public abstract String getDocumentRoleTypeCode()
```
Description copied from interface: UnitAclLoadable

Returns the type code of the document (i.e. Proposal, Protocol, etc).

Specified by:

getDocumentRoleTypeCode in interface Permissionable

Specified by:

getDocumentRoleTypeCode in interface UnitAclLoadable

Returns:
typeCode of document
See Also:
UnitAclLoadable.getDocumentRoleTypeCode()

populateAdditionalQualifiedRoleAttributes
```
public void populateAdditionalQualifiedRoleAttributes(Map<String,String> qualifiedRoleAttributes)
```
Description copied from interface: Permissionable

Allows a permissionable to set additional qualified role attributes that may be needed by kim services to resolve the role members.

Specified by:

populateAdditionalQualifiedRoleAttributes in interface Permissionable

isNew
```
public boolean isNew()
```

isAmendment
```
public boolean isAmendment()
```

isRenewal
```
public boolean isRenewal()
```

isRenewalWithoutAmendment

public boolean isRenewalWithoutAmendment()

getAmendedProtocolNumber
```
public String getAmendedProtocolNumber()
```
If the protocol document is an amendment or renewal the parent protocol number is being returned. (i.e. the protocol number of the protocol that is being amended or renewed). Null will be returned if the protocol is not an amendment or renewal.

Returns:
protocolNumber of the ProtocolBase that is being amended/renewed

isVersioningRequired
```
public boolean isVersioningRequired()
```
Decides whether or not the ProtocolBase is in a state where changes will require versioning. For example: has the protocol had a change in status and not been versioned yet?

Returns:
true if versioning required false if not.

getActiveAttachmentProtocols
```
public List<ProtocolAttachmentProtocolBase> getActiveAttachmentProtocols()
```
This method will return the list of all active attachments for this protocol; an attachment A is active for a protocol if either A has a doc status code of 'draft' or if for all other attachments for that protocol having the same doc id as A's doc id, none have a version number greater than A's version number. is defined as the o

Returns:

getActiveAttachmentProtocolsNoDelete
```
public List<ProtocolAttachmentProtocolBase> getActiveAttachmentProtocolsNoDelete()
```
This method will return the list of undeleted attachments that are still active for this protocol. Essentially it filters out all the deleted elements from the list of active attachments. See getActiveAttachmentProtocols() for a specification of what is an 'active attachment'.

Returns:

isCorrectionMode
```
public boolean isCorrectionMode()
```

setCorrectionMode

public void setCorrectionMode(boolean correctionMode)

getDateTimeService

protected org.kuali.rice.core.api.datetime.DateTimeService getDateTimeService()

getSequenceAccessorService

protected org.kuali.rice.krad.service.SequenceAccessorService getSequenceAccessorService()

getNotifyIrbSubmissionId

public Long getNotifyIrbSubmissionId()

setNotifyIrbSubmissionId

public void setNotifyIrbSubmissionId(Long notifyIrbSubmissionId)

isLookupPendingProtocol

public boolean isLookupPendingProtocol()

setLookupPendingProtocol

public void setLookupPendingProtocol(boolean lookupPendingProtocol)

isLookupPendingPIActionProtocol

public boolean isLookupPendingPIActionProtocol()

setLookupPendingPIActionProtocol

public void setLookupPendingPIActionProtocol(boolean lookupPendingPIActionProtocol)

isLookupActionAmendRenewProtocol

public boolean isLookupActionAmendRenewProtocol()

setLookupActionAmendRenewProtocol

public void setLookupActionAmendRenewProtocol(boolean lookupActionAmendRenewProtocol)

isLookupActionRequestProtocol

public boolean isLookupActionRequestProtocol()

setLookupActionRequestProtocol

public void setLookupActionRequestProtocol(boolean lookupActionRequestProtocol)

isLookupProtocolPersonId

public boolean isLookupProtocolPersonId()

setLookupProtocolPersonId

public void setLookupProtocolPersonId(boolean lookupProtocolPersonId)

isFollowupAction
```
public boolean isFollowupAction(String actionTypeCode)
```
This method is to check if the actiontypecode is a followup action.

Parameters:
actionTypeCode -

Returns:

isMergeAmendment
```
public boolean isMergeAmendment()
```

setMergeAmendment

public void setMergeAmendment(boolean mergeAmendment)

getProtocolAttachmentFilter

public ProtocolAttachmentFilterBase getProtocolAttachmentFilter()

setProtocolAttachmentFilter

public void setProtocolAttachmentFilter(ProtocolAttachmentFilterBase protocolAttachmentFilter)

getFilteredAttachmentProtocols
```
public List<ProtocolAttachmentProtocolBase> getFilteredAttachmentProtocols()
```
This method returns a list of attachments which respect the sort filter

Returns:
a filtered list of protocol attachments

initializeProtocolAttachmentFilter

public abstract void initializeProtocolAttachmentFilter()

getParameterService

public org.kuali.rice.coreservice.framework.parameter.ParameterService getParameterService()

cleanupSpecialReviews

public void cleanupSpecialReviews(ProtocolBase srcProtocol)

isMemberInProtocolPersonnel
```
public boolean isMemberInProtocolPersonnel(CommitteeMembershipBase member)
```
This method encapsulates the logic to decide if a committee member appears in the list of protocol personnel. It will first try to match by personIds and if personIds are not available then it will try matching by rolodexIds.

Parameters:
member -

Returns:

filterOutProtocolPersonnel
```
public List<CommitteeMembershipBase> filterOutProtocolPersonnel(List<CommitteeMembershipBase> members)
```
This method will filter out this protocol's personnel from the given list of committee memberships

Parameters:
members -

Returns:
the filtered list of members

getApplicationDate
```
public Date getApplicationDate()
```
This method is to return the first submission date as application date. see kccoi-36 comment

Returns:

getProjectName
```
public String getProjectName()
```
Description copied from interface: Disclosurable

This method is mainly to get the title

Specified by:

getProjectName in interface Disclosurable

Returns:

getProjectId
```
public String getProjectId()
```
Description copied from interface: Disclosurable

This method to get project number

Specified by:

getProjectId in interface Disclosurable

Returns:

getSortedActions

public List<ProtocolActionBase> getSortedActions()

isEmptyProtocolResearchAreas

public boolean isEmptyProtocolResearchAreas()

isUserNamedInProtocol

public boolean isUserNamedInProtocol(String principalName)

Class ProtocolBase

Field Summary

Fields inherited from class org.kuali.kra.bo.KraPersistableBusinessObjectBase

Fields inherited from class org.kuali.rice.krad.bo.PersistableBusinessObjectBase

Fields inherited from interface org.kuali.kra.common.permissions.Permissionable

Constructor Summary

Method Summary

Methods inherited from class org.kuali.kra.bo.KraPersistableBusinessObjectBase

Methods inherited from class org.kuali.rice.krad.bo.PersistableBusinessObjectBase

Methods inherited from class org.kuali.rice.krad.bo.BusinessObjectBase

Methods inherited from class java.lang.Object

Methods inherited from interface org.kuali.kra.krms.KcKrmsContextBo

Methods inherited from interface org.kuali.rice.core.api.mo.ModelObjectBasic

Field Detail

AMENDMENT_LETTER

RENEWAL_LETTER

NEXT_ACTION_ID_KEY

Constructor Detail

ProtocolBase

Method Detail

getInitiatorLastUpdated

getProtocolSubmissionStatus

getProtocolStatusNewInstanceHook

getDefaultProtocolStatusCodeHook

getDefaultProtocolTypeCodeHook

getProtocolId

setProtocolId

getProtocolNumber

setProtocolNumber

getSequenceNumber

setSequenceNumber

setActive

isActive

getProtocolTypeCode

setProtocolTypeCode

getProtocolStatusCode

setProtocolStatusCode

getTitle

setTitle

getDescription

setDescription

getSubmissionDate

getInitialSubmissionDate

setInitialSubmissionDate

getApprovalDate

setApprovalDate

getExpirationDate

setExpirationDate

getLastApprovalDate

setLastApprovalDate

getFdaApplicationNumber

setFdaApplicationNumber

getReferenceNumber1

setReferenceNumber1

getReferenceNumber2

setReferenceNumber2

getSpecialReviewIndicator

setSpecialReviewIndicator

getKeyStudyPersonIndicator

setKeyStudyPersonIndicator

getFundingSourceIndicator

setFundingSourceIndicator

getCorrespondentIndicator

setCorrespondentIndicator

getReferenceIndicator

setReferenceIndicator

getRelatedProjectsIndicator

setRelatedProjectsIndicator

getProtocolOnlineReviews

getProtocolStatus

setProtocolStatus

getProtocolType

setProtocolType

getNewDescription

setNewDescription

getDefaultNewDescription

setProtocolResearchAreas

getProtocolResearchAreas

addProtocolResearchAreas

getProtocolResearchAreas